To facilitate the histologic analysis of large numbers of 7-day-old zebrafish (Danio rerio), a method has been developed to process them in agarose-embedded arrays. Using thin tissue sections, the morphology of cells and tissues can be examined microscopically to investigate a variety of biologic processes. Because of their small size, precise arrangement of the larvae is necessary to section them simultaneously. A technique was designed to embed groups of zebrafish larvae in a single plane in agarose before sectioning. Stained tissue sections of thousands of larvae can be examined efficiently using this embedding method. In addition to histologic analysis, PCR-based genotypic analysis of DNA from individual larval sections is also possible. This technique can be modified to accommodate any study that requires the histologic examination of many pieces of tissue.